This revised project is concerned with developing new statistical methodology for population genetic data. Attention will be focused on three main areas: the characterization of population structure, the characterization of the association patterns within and between genetic markers and along haplotypes, and the characterization of the identity status of sets of more than two alleles. Theory will be developed at least in part in response to the needs of current large-scale SNP surveys of humans and other species. Specific topics include determining the sampling properties of population-specific measures of population structure and the comparison of marker- and trait-based estimates of population structure. A comparison will be conducted of current methods for defining haplotype blocks, and consideration of alternative methods based on diversity or on contingency-table and regression analyses of one marker versus haplotypes of subsequent markers. The means for drawing inferences about associations among more than two alleles at one locus, or among single alleles taken from multiple loci will be developed.